Difference between revisions of "Molecule model build"

Revision as of 16:20, 15 March 2010

links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages

Proposed starting model

This model addresses the small_molecule class, or part of it, that was discussed in the 2007 WB grant.
Propose a shorter name if you care to.

This is the original model proposed by Anthony so that small molecules can be included on process pages
//
// ?Molecule
// Name ?Text
// Public_name ?Text
// Synonym ?Text
// DB_info Database ?Database ?Database_field ?Accession_number
// Involved_in_process ?WBProcess XREF Molecule
//
If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to
be attached directly to the process model, so the following model omits the WBProcess XREF.

///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?Sm_molecule
//  * metabolites: precursors, intermediates, or end products of a metabolic pathway
//  * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
//  * chemicals/drugs
//  * minerals, ions, salts
//
////////////////////////////////////////////////////////////////////////////////////
?Sm_molecule	Name ?Text 
		Synonym ?Text 
		DB_info Database ?Database ?Database_field ?Accession_number 
               //Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence -- Add Sm_molecule to Phenotype Assay? If so, do we need a XREF here?
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator #Evidence
               //Microarray_experiment -- can this be done by adding Sm_molecule to  ?Condition? 
               Reference ?Paper XREF Sm_molecule
///////////////////////////////////////////////////////////////////////////////////

Model elements

Name-> WBSMolID, is this necessary?
Public name -> prevalent name in elegans literature, or is this redundant with Synonym?
Synonym -> other names, how do we mine these from other DBs?
DB_info -> links to entity in other database add following databases to database.ace
- ChEBI used in Reactome http://www.ebi.ac.uk/chebi/init.do
  - does not have daumone, ascarosides
- KEGG COMPOUND used in Reactome/ nemapath http://www.genome.jp/kegg/
- PubChem used in Reactome hhtp://www.pubchem.ncbi.nlm.nih.gov/
  - has ascarosides but might not be the ones purified from elegans
- Klotho (?)used for BioCyc http://www.biocheminfo.org/klotho/accession_table.html
- KDR http://www.kdr.co.kr
  - for daumone http://www.kdr.co.kr/Daumone/main.asp

If a Sm_molecule tag is added to the following classes, do we need a XREF in the Sm_molecule model?

Phenotype Phenotype_assay ?Phenotype_info
Gene_regulation --to annotate chemicals as regulators of gene activity
Microarray_experiment ?Condition -- to capture chemical/drug treatment to large scale gene expression studies
Paper -- for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here

Possible model elements

KEGG ID (enzyme classification) , Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.
Vendors/Sources //This information should be linked to a particular experiment and therefore paper?
- Sigma-Aldrich
- MP Biochemicals
- Calbiochem
- ZINC

Other databases

Enzyme database? http://ca.expasy.org/enzyme/enzyme-bycompound.html
DrugBank found in pubchem http://www.drugbank.ca/
LeadScope found in pubchem http://www.leadscope.com/
EPA found in pubchem http://www.epa.gov/ncct/dsstox/
NIH Small molecule repository found in pubchem http://mlsmr.glpg.com/MLSMR_HomePage/
Nature chemical biology found in pubchem http://www.nature.com/nchembio/index.html
NIH chemical genomics center found in pubchem http://ncgc.nih.gov/db/
see pubchem compounds for more

@@ Line 5: / Line 5: @@
 ----
 ==Proposed starting model==
-This model the addresses small_molecule class, or part of it, that was discussed in the 2007 WB grant.<br>
+This model addresses the small_molecule class, or part of it, that was discussed in the 2007 WB grant.<br>
 ''Propose a shorter name if you care to.''<br>
 -----<br>
-Original model proposed by Anthony so that small molecules can be included on process pages<br>
+This is the original model proposed by Anthony so that small molecules can be included on process pages<br>
+//<br>
 // ?Molecule<br>
 //         Name ?Text<br>
+//         Public_name ?Text<br>
 //         Synonym ?Text<br>
 //         DB_info Database ?Database ?Database_field ?Accession_number<br>
 //         Involved_in_process ?WBProcess XREF Molecule<br>
-// -----<br>
+//<br>
 If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to <br>
-be attached directly to the process pages, so the following model omits the process page XREF.<br>
+be attached directly to the process model, so the following model omits the WBProcess XREF.<br>
@@ Line 22: / Line 24: @@
   //
   // ?Sm_molecule
-  //
+  //  * metabolites: precursors, intermediates, or end products of a metabolic pathway
+ //  * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
+ //  * chemicals/drugs
+ //  * minerals, ions, salts
   //
   ////////////////////////////////////////////////////////////////////////////////////
   ?Sm_molecule	Name ?Text
   		Synonym ?Text
-  		DB_info Database ?Database ?Database_field ?Accession_number // link to the actual entity page in the DB
+  		DB_info Database ?Database ?Database_field ?Accession_number
-                Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Follows example from other Phenotype_info Phenotype_assay tags
+                //Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence -- Add Sm_molecule to Phenotype Assay? If so, do we need a XREF here?
-                 Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Follows example of other objects in Regulator sub-class of gene regulation
+                 Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator #Evidence
-                 //Microarray_experiment.  can this be done through ?Condition?
+                 //Microarray_experiment -- can this be done by adding Sm_molecule to  ?Condition?
-                 Reference ?Paper XREF Sm_molecule #Evidence //This is to attach a sm_molecule to a paper in a similar way to attaching a gene to a paper, not to make a reference to this sm_molecule itself.
+                 Reference ?Paper XREF Sm_molecule
   ///////////////////////////////////////////////////////////////////////////////////
-----
-Small Molecule:
-* metabolites: precursors, intermediates, or end products of a metabolic pathway
-* monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
-* chemicals/drugs
-* minerals, ions, salts
-----
-Name = WBSMol ID <br>
-Common name = most prevalent name in elegans literature <br>
-Synonym = other names mined from other databases, literature, etc. :: how to mine these names in bulk? <br>
-DB_info  = mappings to chemical databases, see databases to add via database.ace file below, no XREF needed? <br>
-Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule ::  no XREF needed in Phenotype_info<br>
-Gene_regulation Regulator_chemical ?Gene_regulation :: to annotate chemical based gene regulation :: XREF needed<br>
-Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?<br>
-Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here :: XREF needed<br>
-----
-Databases
-* ChEBI
-**does not have daumone, ascarosides
-* PubChem
-** has ascarosides but might not be the ones purified from elegans
-* KDR
-** for daumone http://www.kdr.co.kr/Daumone/main.asp
 ==Model elements==
-Name-> do we want a WBID for this class<br>
+* Name->  WBSMolID, is this necessary?
-Synonym -> public/common names<br>
+* Public name -> prevalent name in elegans literature, or is this redundant with Synonym?
-DB_info  links to other databases and database ID's  <br>
+* Synonym -> other names, how do we mine these from other DBs?
-* ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
+* DB_info  -> links to entity in other database add following databases to database.ace
-* KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/
+** ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
-* PubChem  ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/
+***does not have daumone, ascarosides
-* Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
+** KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/
+** PubChem  ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/
+*** has ascarosides but might not be the ones purified from elegans
+** Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
+** KDR http://www.kdr.co.kr
+*** for daumone http://www.kdr.co.kr/Daumone/main.asp
+If a Sm_molecule tag is added to the following classes, do we need a XREF in the Sm_molecule model?
+* Phenotype Phenotype_assay ?Phenotype_info
+* Gene_regulation  --to annotate chemicals as regulators of gene activity
+* Microarray_experiment ?Condition -- to capture chemical/drug treatment to large scale gene expression studies
+* Paper -- for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here
 ===Possible model elements===
-KEGG ID  (enzyme classification) ,  Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.  <br>
+* KEGG ID  (enzyme classification) ,  Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.
-Vendors/Sources //This information should be linked to a particular experiment and therefore paper.<br>
+* Vendors/Sources //This information should be linked to a particular experiment and therefore paper?
-* Sigma-Aldrich
+** Sigma-Aldrich
-* MP Biochemicals
+** MP Biochemicals
-* Calbiochem
+** Calbiochem
-* ZINC
+** ZINC
 Other databases

Difference between revisions of "Molecule model build"

Revision as of 16:20, 15 March 2010

Contents

Proposed starting model

Model elements

Possible model elements

Chris's notes

Jolene's notes

Raymond's notes

Karen's notes

General concerns and comments

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